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Dicty_cDB
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NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
SHF860
Library SH
(Link to library)
Clone ID SHF860
Atlas ID -
NBRP ID -
dictyBase ID -
Link to Contig Contig-U16581-1
Original site URL
Representative seq. ID SHF860P
(Link to Original site)
Representative DNA sequence 
>SHF860 (SHF860Q) /CSM/SH/SHF8-C/SHF860Q.Seq.d/
CTTTTTGGTGCTTCTGTTAAGCTAATGCTAAGGTGTCTCTCTCCCCCTTTGCTTTGCATT
ACTCTCCTCAAGCTCAGATAATCTCGAGCTCCACTAACGATGCTCCTCAAGTATCCTCAG
GGTTAATCCATCACATTCCTATGCAACTCTCTCAAATGTATAAGCAGTCTTTAACAAAAA
AAAATATTTAAAAAAAAAAXXXXXXXXXXCTTTTTGGTGCTTCTGTTAAGATAATGATAA
GGTGTCTNTNTCCCCCTTTGCTTTGCATTACTCTCCTCAAGCTCAGATAATCTCGAGCTC
CACTAACGATGCTCCTCAAGTATCCTCAGGGTTAATCCATCACATTCCTATGCAACTCTC
TCAAATGTATAAGCAGTCTTTAACAAAAAAAAAT
sequence update 2002.10.25
Translated Amino Acid sequence 
flvllls*c*gvslplcfallssssdnlelh*rcsssilrvnpshsyatlsnv*AVFNKK
KYLKKK---

---LFGASVKIMIRCLXPPLLCITLLKLR*srapltmllkypqg*sitflcnslkcissl
*qkk
Translated Amino Acid sequence (All Frames) 
Frame A:
lfgasvklmlrclsppllcitllklr*srapltmllkypqg*sitflcnslkcissl*qk
kifkkk---

---LFGASVKIMIRCLXPPLLCITLLKLR*srapltmllkypqg*sitflcnslkcissl
*qkk

Frame B:
flvllls*c*gvslplcfallssssdnlelh*rcsssilrvnpshsyatlsnv*AVFNKK
KYLKKK---

---flvlllr***gvxxplcfallssssdnlelh*rcsssilrvnpshsyatlsnv*avf
nkkk

Frame C:
fwcfc*anakvslspfalhyspqaqiissstndapqvssglihhipmqlsqmykqsltkk
ni*kk---

---fwcfc*dndkvsxspfalhyspqaqiissstndapqvssglihhipmqlsqmykqsl
tkkn
Homology vs CSM-cDNA 

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

VSA585 (VSA585Q) /CSM/VS/VSA5-D/VSA585Q.Seq.d/                        347   8e-95
SSM728 (SSM728Q) /CSM/SS/SSM7-B/SSM728Q.Seq.d/                        347   8e-95
SSM719 (SSM719Q) /CSM/SS/SSM7-A/SSM719Q.Seq.d/                        347   8e-95
SSM276 (SSM276Q) /CSM/SS/SSM2-D/SSM276Q.Seq.d/                        347   8e-95
SSM269 (SSM269Q) /CSM/SS/SSM2-C/SSM269Q.Seq.d/                        347   8e-95
SSM229 (SSM229Q) /CSM/SS/SSM2-B/SSM229Q.Seq.d/                        347   8e-95
SSM165 (SSM165Q) /CSM/SS/SSM1-C/SSM165Q.Seq.d/                        347   8e-95
SSL845 (SSL845Q) /CSM/SS/SSL8-B/SSL845Q.Seq.d/                        347   8e-95
SSL836 (SSL836Q) /CSM/SS/SSL8-B/SSL836Q.Seq.d/                        347   8e-95
SSL768 (SSL768Q) /CSM/SS/SSL7-C/SSL768Q.Seq.d/                        347   8e-95
own update 2004. 8.24
Homology vs DNA 

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

D16417|D16417.1 Dictyostelium discoideum mRNA.                    347   1e-91  1
BZ463651|BZ463651.1 BONRK12TR BO_1.6_2_KB_tot Brassica oleracea genomic clone BONRK12, DNA sequence.    50   0.037  1
CC173933|CC173933.1 ZMMBBc0306H18r ZMMBBc Zea mays subsp. mays genomic clone ZMMBBc0306H18 3', DNA sequence.    34   0.78   2
N68478|N68478.1 za14f01.s1 Soares fetal liver spleen 1NFLS Homo sapiens cDNA clone IMAGE:292537 3', mRNA sequence.    32   6.2    2
BU291705|BU291705.1 604167080F1 CSEQCHN55 Gallus gallus cDNA clone ChEST1027p19 5', mRNA sequence.    32   7.8    2
CX300859|CX300859.1 C08003A05SK PhyRootSw1 Citrus sinensis cDNA clone C08003A05, mRNA sequence.    34   7.8    2
CF886999|CF886999.1 UI-CF-DU1-abf-e-20-18-UI.r18 UI-CF-DU1 Homo sapiens cDNA clone UI-CF-DU1-abf-e-20-18-UI 5', mRNA sequence.    32   8.9    2
AC172899|AC172899.2 Bos taurus clone CH240-502O12, *** SEQUENCING IN PROGRESS ***, 41 unordered pieces.    42   9.1    1
AC093987|AC093987.6 Rattus norvegicus clone CH230-36D18, WORKING DRAFT SEQUENCE, 5 unordered pieces.    42   9.1    1
AJ871882|AJ871882.1 Coffea canephora subsp. canephora microsatellite DNA, clone 81D07.    42   9.1    1
dna update 2006. 3.23
Homology vs Protein 

 ***** No hits found ******

Lambda     K      H
   0.318    0.134    0.401

Gapped
Lambda     K      H
   0.267   0.0410    0.140

Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3039690
Number of Hits to DB: 432,528,225
protein update 2009. 4.18
PSORT 

 psg: 0.70  gvh: 0.53  alm: 0.35  top: 0.53  tms: 0.00  mit: 0.42  mip: 0.00
 nuc: 0.12  erl: 0.00  erm: 0.20  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 0.00  tyr: 0.00  leu: 0.00  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 0.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 1.00 

	 40.0 %: mitochondrial
	 32.0 %: nuclear
	 16.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: vacuolar
	  4.0 %: plasma membrane

>> prediction for SHF860 is mit
5' end seq. ID SHF860F
5' end seq. 
>SHF860F.Seq
CTTTTTGGTGCTTCTGTTAAGCTAATGCTAAGGTGTCTCTCTCCCCCTTTGCTTTGCATT
ACTCTCCTCAAGCTCAGATAATCTCGAGCTCCACTAACGATGCTCCTCAAGTATCCTCAG
GGTTAATCCATCACATTCCTATGCAACTCTCTCAAATGTATAAGCAGTCTTTAACAAAAA
AAAATATTTAAAAAAAAAANNNNNNNNNN
Length of 5' end seq. 209
3' end seq. ID SHF860Z
3' end seq. 
>SHF860Z.Seq
NNNNNNNNNNCTTTTTGGTGCTTCTGTTAAGATAATGATAAGGTGTCTNTNTCCCCCTTT
GCTTTGCATTACTCTCCTCAAGCTCAGATAATCTCGAGCTCCACTAACGATGCTCCTCAA
GTATCCTCAGGGTTAATCCATCACATTCCTATGCAACTCTCTCAAATGTATAAGCAGTCT
TTAACAAAAAAAAAT
Length of 3' end seq. 195
Connected seq. ID SHF860P
Connected seq. 
>SHF860P.Seq
CTTTTTGGTGCTTCTGTTAAGCTAATGCTAAGGTGTCTCTCTCCCCCTTTGCTTTGCATT
ACTCTCCTCAAGCTCAGATAATCTCGAGCTCCACTAACGATGCTCCTCAAGTATCCTCAG
GGTTAATCCATCACATTCCTATGCAACTCTCTCAAATGTATAAGCAGTCTTTAACAAAAA
AAAATATTTAAAAAAAAAA----------CTTTTTGGTGCTTCTGTTAAGATAATGATAA
GGTGTCTNTNTCCCCCTTTGCTTTGCATTACTCTCCTCAAGCTCAGATAATCTCGAGCTC
CACTAACGATGCTCCTCAAGTATCCTCAGGGTTAATCCATCACATTCCTATGCAACTCTC
TCAAATGTATAAGCAGTCTTTAACAAAAAAAAAT
Length of connected seq. 384
Full length Seq ID -
Full length Seq. -
Length of full length seq. -